Variant report

Variant	rs72886553
Chromosome Location	chr2:183807427-183807428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:183805979-183808718	K562	blood:	n/a	n/a
2	POLR2A	chr2:183807422-183807496	MCF10A-Er-Src	breast:	n/a	n/a
3	EP300	chr2:183805730-183807874	SK-N-SH	brain:	n/a	chr2:183807650-183807664 chr2:183806893-183806907 chr2:183806895-183806909 chr2:183807447-183807461 chr2:183805856-183805870 chr2:183805953-183805967 chr2:183806038-183806052 chr2:183807461-183807475
4	MXI1	chr2:183805959-183808373	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:183805862..183807763-chr2:183903023..183904588,2	K562	blood:
2	chr2:183798092..183800386-chr2:183804710..183808367,3	K562	blood:

Variant related genes	Relation type
NCKAP1	TF binding region
ENSG00000061676	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1473614	0.86[EUR][1000 genomes]
rs1473615	0.86[EUR][1000 genomes]
rs1473616	0.86[EUR][1000 genomes]
rs2675054	0.86[EUR][1000 genomes]
rs2705715	0.86[EUR][1000 genomes]
rs2705718	0.86[EUR][1000 genomes]
rs2705719	0.86[EUR][1000 genomes]
rs2705720	0.86[EUR][1000 genomes]
rs2705721	0.86[EUR][1000 genomes]
rs35142583	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36077496	1.00[AMR][1000 genomes]
rs55657876	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55696219	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55764044	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55957340	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56152140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56182353	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6707761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6712479	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6743323	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6750392	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72886518	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72886527	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72886538	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72886541	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72886545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72886547	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72886557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72886568	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72886577	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72886596	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72886600	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72888431	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72888449	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72888452	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72888461	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72888464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72888472	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72888474	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72888478	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72888481	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72888488	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72888489	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72890307	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72890315	1.00[AFR][1000 genomes]
rs72890345	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72890349	0.87[AMR][1000 genomes]
rs72890352	1.00[AMR][1000 genomes]
rs72890353	1.00[AMR][1000 genomes]
rs72890370	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72890384	1.00[AMR][1000 genomes]
rs72890392	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72890398	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72892604	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72892631	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72892638	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72892656	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72892689	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72892694	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72892702	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72894503	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72894513	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72894523	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72894527	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72894533	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72894535	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72894537	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72894539	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72894544	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72894546	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72894570	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72894585	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72894593	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72894596	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72896508	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72896517	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72896518	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72896520	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72896524	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72896528	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72896534	0.86[EUR][1000 genomes]
rs72900766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72900772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72900775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72900780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7562034	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7565260	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7566497	1.00[AMR][1000 genomes]
rs7567370	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7577407	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2757842	chr2:183437700-183835084	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759104	chr2:183437700-183835084	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv818096	chr2:183701588-183827018	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	esv3693446	chr2:183785598-183833514	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv1005281	chr2:183803173-184093877	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv3331357	chr2:183807368-183807791	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183768600-183811600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr2:183769800-183811800	Weak transcription	Small Intestine	intestine
3	chr2:183772400-183811800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:183773400-183866000	Weak transcription	Colonic Mucosa	Colon
5	chr2:183773400-183877800	Weak transcription	Stomach Mucosa	stomach
6	chr2:183775600-183833000	Weak transcription	Pancreas	Pancrea
7	chr2:183780400-183874800	Weak transcription	Esophagus	oesophagus
8	chr2:183780800-183811200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:183782200-183814200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:183784800-183811400	Strong transcription	Fetal Intestine Large	intestine
11	chr2:183785800-183824200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:183786400-183814200	Weak transcription	Aorta	Aorta
13	chr2:183786600-183826600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:183787000-183824000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr2:183788000-183830000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:183788200-183845600	Weak transcription	Lung	lung
17	chr2:183788400-183809600	Strong transcription	NH-A	brain
18	chr2:183788400-183811600	Weak transcription	Right Ventricle	heart
19	chr2:183789200-183836400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:183789400-183811600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:183789600-183812600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:183790200-183814400	Weak transcription	Brain Hippocampus Middle	brain
23	chr2:183790800-183824200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:183791200-183808600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:183792600-183811400	Weak transcription	Hela-S3	cervix
26	chr2:183793200-183811600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:183793200-183811600	Weak transcription	Brain Substantia Nigra	brain
28	chr2:183793400-183811000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:183793400-183840800	Weak transcription	Fetal Brain Male	brain
30	chr2:183793600-183811600	Weak transcription	Psoas Muscle	Psoas
31	chr2:183793600-183814400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:183793600-183823800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:183793600-183826600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:183794600-183808200	Strong transcription	HepG2	liver
35	chr2:183795200-183824200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr2:183795400-183814600	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:183795400-183857600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr2:183796800-183811600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr2:183798600-183811800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:183798600-183812000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr2:183798600-183814200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:183798600-183847000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:183799600-183811600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:183800200-183817200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr2:183800400-183812600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:183802600-183814000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:183802800-183811400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr2:183802800-183814400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:183802800-183817800	Weak transcription	Fetal Brain Female	brain
50	chr2:183803000-183811200	Weak transcription	Osteobl	bone

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